class: center, middle, inverse, title-slide .title[ # R Markdown and Git/GitHub ] .author[ ### MACSS 30500 <br /> University of Chicago ] --- class: middle --- ## R Markdown: resources Assigned readings: * Chapters 27 "R Markdown", 28 "Graphics for communication", and 29 "R Markdown formats" in [R for Data Science](http://r4ds.had.co.nz) Additional resources: * [R Markdown the definitive Guide](https://bookdown.org/yihui/rmarkdown/) * [R Markdown cheat sheet](https://posit.co/resources/cheatsheets/?_page=2/) * [Markdown and R Markdown](https://pjbartlein.github.io/REarthSysSci/markdown.html) by Pat Bartlein * [R Markdown from R Studio](https://rmarkdown.rstudio.com/lesson-1.html) official documentation * `Rmarkdown.Rmd` from Lecture 2 `usethis::use_course("css-materials/intro-r")` --- ## R Markdown and Markdown **R Markdown**: text file that uses the extension `.Rmd`. **Markdown**: text file that use the extension `.md` * Similarities: * they use the same syntax, R Markdown is just an extension of the markdown syntax * Differences: * R code cannot be executed in a `.md` VS we can embed and execute R code in a `.Rmd ` * An `.md` can be generated from a `.Rmd` but not the other way around --- ## R Markdown: Knitting process R Markdown files allow to generate well-formatted documents (md, pdf, word, html, etc.) that include text, code, and output. To create such documents, you “Knit” or “render” them in three ways: 1. by clicking the “Knit” button in the script editor panel of your R Markdown file and select the desired output 1. by adding the desired output in the YAML header such as: `github_document`, `pdf_document`, `word_document`, `html_document`, etc. (notice: without `\(\LaTeX\)` installed, the pdf won't work) 1. by using `render()`, as explained [here](https://pkgs.rstudio.com/rmarkdown/reference/render.html). For example, run in your console: `rmarkdown::render("my-document.Rmd", output_format: html_document`) --- ## R Markdown: Knitting process for presentations * [ioslides](http://rmarkdown.rstudio.com/ioslides_presentation_format.html) * [reveal.js](http://rmarkdown.rstudio.com/revealjs_presentation_format.html) * [Slidy](http://rmarkdown.rstudio.com/slidy_presentation_format.html) * [Beamer](http://rmarkdown.rstudio.com/beamer_presentation_format.html) * [`xaringan`](https://bookdown.org/yihui/rmarkdown/xaringan.html) --- ## R Markdown: Knitting process <img src="rmarkdownflow.png" width="80%" style="display: block; margin: auto;" />